Emission Object is in front of every other object
Please consider using the [alpha over node].

For transparency in Cycles render use Panel Film Transparent.



[ Alpha over node ] respects transparency alpha.  In your example opaque black cube would be opaque over all parts of the blurred white cube.

Alpha is transparency and its effects are only visible by compositing two or more layers.

In the image above the white emission cube in layer 2 is blurred.  The sphere and yellow emission cube are in layer 1.  Yellow emission is to increase legibility of explanation.

Two render layer specifications use different visual scene layers in the image below. (Layers and Scenes have some difficult terminology in Blender which could be improved)



3D Views with object visibility in layers in the image below.



Note the checkered background for transparency. Using [object index] is a complement or replacement to layers.